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#1 2018-02-25 09:24:19

freebe
Member
From: Germany
Registered: 2015-10-29
Posts: 41

pacman error message "ldconfig: File *** is empty, not checked"

Dear Arch community,

I've been getting these error-messages now for some time after I upgrade or install a package with pacman.

ldconfig: File /usr/lib/libnautilus-extension.so is empty, not checked.
ldconfig: File /usr/lib/libisoburn.so is empty, not checked.
ldconfig: File /usr/lib/libixion-0.13.so is empty, not checked.
ldconfig: File /usr/lib/libmediaart-2.0.so is empty, not checked.
ldconfig: File /usr/lib/libmediaart-2.0.so.0 is empty, not checked.
ldconfig: File /usr/lib/libnautilus-extension.so.1 is empty, not checked.
ldconfig: File /usr/lib/libisoburn.so.1.105.0 is empty, not checked.
ldconfig: File /usr/lib/libnautilus-extension.so.1.4.0 is empty, not checked.
ldconfig: File /usr/lib/libmediaart-2.0.so.0.904.0 is empty, not checked.
ldconfig: File /usr/lib/libixion-0.13.so.0.0.0 is empty, not checked.
ldconfig: File /usr/lib/libixion-0.13.so.0 is empty, not checked.
ldconfig: File /usr/lib/libisoburn.so.1 is empty, not checked.
ldconfig: File /usr/lib32/libgcc_s.so is empty, not checked.
ldconfig: File /usr/lib32/libatomic.so.1.2.0 is empty, not checked.
ldconfig: File /usr/lib32/libgfortran.so is empty, not checked.
ldconfig: File /usr/lib32/libgfortran.so.4.0.0 is empty, not checked.
ldconfig: File /usr/lib32/libgcc_s.so.1 is empty, not checked.
ldconfig: File /usr/lib32/libcilkrts.so.5.0.0 is empty, not checked.
ldconfig: File /usr/lib32/libgfortran.so.4 is empty, not checked.
ldconfig: File /usr/lib32/libatomic.so.1 is empty, not checked.
ldconfig: File /usr/lib32/libatomic.so is empty, not checked.
ldconfig: File /usr/lib32/libcilkrts.so.5 is empty, not checked.
ldconfig: File /usr/lib32/libcilkrts.so is empty, not checked.

I have no Idea where that error is coming from. Looking in the directory I find that the files are not empty, the symbolic links seem to point to valid files.

For example ibcilkrts.so:

lrwxrwxrwx   1 root root       19 26. Jan 22:05 libcilkrts.so -> libcilkrts.so.5.0.0
lrwxrwxrwx   1 root root       19 26. Jan 22:05 libcilkrts.so.5 -> libcilkrts.so.5.0.0
-rwxr-xr-x   1 root root   588176 26. Jan 22:05 libcilkrts.so.5.0.0
-rw-r--r--   1 root root      173 26. Jan 22:04 libcilkrts.spec

Does anyone have an Idea where that error is might be coming from? What I could check? I didn't find any clue in the archwiki nor via google. I don't have libxfont, only libxfont2. Multilib is enabled. I use gnome with wayland, if that makes a difference.

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#2 2018-02-25 10:06:05

seth
Member
From: Won't reply 2 private help req
Registered: 2012-09-03
Posts: 78,863

Re: pacman error message "ldconfig: File *** is empty, not checked"

pacman -Qkk

How to upload text · How to boot w/o GUI · Disable Windows Fast-Start! · Fix your xinitrc

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#3 2018-02-26 08:48:13

fdservices
Member
From: France
Registered: 2012-02-06
Posts: 413

Re: pacman error message "ldconfig: File *** is empty, not checked"

Did you check libcilkrts.so in /usr/lib32?

Andrew

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#4 2018-02-27 17:51:03

freebe
Member
From: Germany
Registered: 2015-10-29
Posts: 41

Re: pacman error message "ldconfig: File *** is empty, not checked"

Nice! 

pacman -Qkk | grep warning

kind of did the trick! Thank you!

I solved the problem for lib32-gcc-libs, the other packages I didn't touch yet. I uninstalled the lib32-gcc-libs with all it's dependencies, deleted the files contained in the package in /usr/lib32 and then reinstalled lib32-gcc-libs.

I had to manually delete the lib32 files because I got a "conflicting files" error messages. ICan someone tell my why pacman didn't overwrite the old files when I wanted to reinstall the package with 

 "sudo pacman -S lib32-gcc-libs

? And why uninstalling the package didn't delete the files in /usr/lib32/ ?

Is it appropriate in such a situation to just force-reinstall the package?



Thank you and kind regards
freebe

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#5 2018-02-27 18:01:38

loqs
Member
Registered: 2014-03-06
Posts: 19,113

Re: pacman error message "ldconfig: File *** is empty, not checked"

freebe wrote:

I had to manually delete the lib32 files because I got a "conflicting files" error messages. ICan someone tell my why pacman didn't overwrite the old files when I wanted to reinstall the package with 

 "sudo pacman -S lib32-gcc-libs

? And why uninstalling the package didn't delete the files in /usr/lib32/ ?

What was the command you used to reinstall lib32-gcc-libs and the full output it generated containing "conflicting files"?
Edit:
Also what was the output from pacman -Qkk before you attempted to fix the issue? 
grammar add "it generated"

Last edited by loqs (2018-02-27 18:08:17)

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#6 2018-02-28 21:17:08

freebe
Member
From: Germany
Registered: 2015-10-29
Posts: 41

Re: pacman error message "ldconfig: File *** is empty, not checked"

Thanks for the reply!

I didn't save the outputs that I got, but I can reproduce the error with the "libnautilus-extension" package.

So trying to install the package:

sudo pacman -S libnautilus-extension 

warning: libnautilus-extension-3.26.2-3 is up to date -- reinstalling
resolving dependencies...
looking for conflicting packages...

Packages (1) libnautilus-extension-3.26.2-3

Total Installed Size:  0,38 MiB

:: Proceed with installation? [Y/n] y
(1/1) checking keys in keyring                     [######################] 100%
(1/1) checking package integrity                   [######################] 100%
(1/1) loading package files                        [######################] 100%
(1/1) checking for file conflicts                  [######################] 100%
error: failed to commit transaction (conflicting files)
libnautilus-extension: /usr/include/nautilus/libnautilus-extension/nautilus-column-provider.h exists in filesystem
libnautilus-extension: /usr/include/nautilus/libnautilus-extension/nautilus-column.h exists in filesystem
libnautilus-extension: /usr/include/nautilus/libnautilus-extension/nautilus-extension-types.h exists in filesystem
libnautilus-extension: /usr/include/nautilus/libnautilus-extension/nautilus-file-info.h exists in filesystem
libnautilus-extension: /usr/include/nautilus/libnautilus-extension/nautilus-info-provider.h exists in filesystem
libnautilus-extension: /usr/include/nautilus/libnautilus-extension/nautilus-location-widget-provider.h exists in filesystem
libnautilus-extension: /usr/include/nautilus/libnautilus-extension/nautilus-menu-item.h exists in filesystem
libnautilus-extension: /usr/include/nautilus/libnautilus-extension/nautilus-menu-provider.h exists in filesystem
libnautilus-extension: /usr/include/nautilus/libnautilus-extension/nautilus-menu.h exists in filesystem
libnautilus-extension: /usr/include/nautilus/libnautilus-extension/nautilus-property-page-provider.h exists in filesystem
libnautilus-extension: /usr/include/nautilus/libnautilus-extension/nautilus-property-page.h exists in filesystem
libnautilus-extension: /usr/lib/girepository-1.0/Nautilus-3.0.typelib exists in filesystem
libnautilus-extension: /usr/lib/libnautilus-extension.so exists in filesystem
libnautilus-extension: /usr/lib/libnautilus-extension.so.1 exists in filesystem
libnautilus-extension: /usr/lib/libnautilus-extension.so.1.4.0 exists in filesystem
libnautilus-extension: /usr/lib/pkgconfig/libnautilus-extension.pc exists in filesystem
libnautilus-extension: /usr/share/gir-1.0/Nautilus-3.0.gir exists in filesystem
libnautilus-extension: /usr/share/gtk-doc/html/libnautilus-extension/NautilusColumn.html exists in filesystem
libnautilus-extension: /usr/share/gtk-doc/html/libnautilus-extension/NautilusColumnProvider.html exists in filesystem
libnautilus-extension: /usr/share/gtk-doc/html/libnautilus-extension/NautilusFileInfo.html exists in filesystem
libnautilus-extension: /usr/share/gtk-doc/html/libnautilus-extension/NautilusInfoProvider.html exists in filesystem
libnautilus-extension: /usr/share/gtk-doc/html/libnautilus-extension/NautilusLocationWidgetProvider.html exists in filesystem
libnautilus-extension: /usr/share/gtk-doc/html/libnautilus-extension/NautilusMenu.html exists in filesystem
libnautilus-extension: /usr/share/gtk-doc/html/libnautilus-extension/NautilusMenuItem.html exists in filesystem
libnautilus-extension: /usr/share/gtk-doc/html/libnautilus-extension/NautilusMenuProvider.html exists in filesystem
libnautilus-extension: /usr/share/gtk-doc/html/libnautilus-extension/NautilusPropertyPage.html exists in filesystem
libnautilus-extension: /usr/share/gtk-doc/html/libnautilus-extension/NautilusPropertyPageProvider.html exists in filesystem
libnautilus-extension: /usr/share/gtk-doc/html/libnautilus-extension/ch01.html exists in filesystem
libnautilus-extension: /usr/share/gtk-doc/html/libnautilus-extension/home.png exists in filesystem
libnautilus-extension: /usr/share/gtk-doc/html/libnautilus-extension/index.html exists in filesystem
libnautilus-extension: /usr/share/gtk-doc/html/libnautilus-extension/ix01.html exists in filesystem
libnautilus-extension: /usr/share/gtk-doc/html/libnautilus-extension/left-insensitive.png exists in filesystem
libnautilus-extension: /usr/share/gtk-doc/html/libnautilus-extension/left.png exists in filesystem
libnautilus-extension: /usr/share/gtk-doc/html/libnautilus-extension/libnautilus-extension-NautilusModule.html exists in filesystem
libnautilus-extension: /usr/share/gtk-doc/html/libnautilus-extension/libnautilus-extension.devhelp2 exists in filesystem
libnautilus-extension: /usr/share/gtk-doc/html/libnautilus-extension/pt01.html exists in filesystem
libnautilus-extension: /usr/share/gtk-doc/html/libnautilus-extension/right-insensitive.png exists in filesystem
libnautilus-extension: /usr/share/gtk-doc/html/libnautilus-extension/right.png exists in filesystem
libnautilus-extension: /usr/share/gtk-doc/html/libnautilus-extension/style.css exists in filesystem
libnautilus-extension: /usr/share/gtk-doc/html/libnautilus-extension/up-insensitive.png exists in filesystem
libnautilus-extension: /usr/share/gtk-doc/html/libnautilus-extension/up.png exists in filesystem
Errors occurred, no packages were upgraded.

Now uninstall:

sudo pacman -Rc libnautilus-extension
checking dependencies...
:: gnome-shell-extensions optionally requires nautilus: gnome-classic session

Packages (3) gnome-tweak-tool-3.26.4-1  nautilus-3.26.2-3  libnautilus-extension-3.26.2-3

Total Removed Size:  16,08 MiB

:: Do you want to remove these packages? [Y/n] y
:: Processing package changes...
(1/3) removing gnome-tweak-tool                                        [#######################################] 100%
(2/3) removing nautilus                                                [#######################################] 100%
(3/3) removing libnautilus-extension                                   [#######################################] 100%
ldconfig: File /usr/lib/libnautilus-extension.so is empty, not checked.
ldconfig: File /usr/lib/libisoburn.so is empty, not checked.
ldconfig: File /usr/lib/libixion-0.13.so is empty, not checked.
ldconfig: File /usr/lib/libmediaart-2.0.so is empty, not checked.
ldconfig: File /usr/lib/libmediaart-2.0.so.0 is empty, not checked.
ldconfig: File /usr/lib/libnautilus-extension.so.1 is empty, not checked.
ldconfig: File /usr/lib/libisoburn.so.1.105.0 is empty, not checked.
ldconfig: File /usr/lib/libnautilus-extension.so.1.4.0 is empty, not checked.
ldconfig: File /usr/lib/libmediaart-2.0.so.0.904.0 is empty, not checked.
ldconfig: File /usr/lib/libixion-0.13.so.0.0.0 is empty, not checked.
ldconfig: File /usr/lib/libixion-0.13.so.0 is empty, not checked.
ldconfig: File /usr/lib/libisoburn.so.1 is empty, not checked.
:: Running post-transaction hooks...
(1/4) Compiling GSettings XML schema files...
(2/4) Updating icon theme caches...
(3/4) Arming ConditionNeedsUpdate...
(4/4) Updating the desktop file MIME type cache...

Installing all of it again with "sudo pacman -S gnome-tweak-tool nautilus libnautilus-extension" gives the same issues as in the first step. Since gnome-tweak-tool and nautilus are dependencies of libnautilus-extension, I wasn't able to reinstall the other packages now.

[normi@freelinux ~]$ sudo pacman -S gnome-tweak-tool nautilus libnautilus-extension 
resolving dependencies...
looking for conflicting packages...

Packages (3) gnome-tweak-tool-3.26.4-1  libnautilus-extension-3.26.2-3  nautilus-3.26.2-3

Total Installed Size:  16,45 MiB

:: Proceed with installation? [Y/n] y
(3/3) checking keys in keyring                                         [#######################################] 100%
(3/3) checking package integrity                                       [#######################################] 100%
(3/3) loading package files                                            [#######################################] 100%
(3/3) checking for file conflicts                                      [#######################################] 100%
error: failed to commit transaction (conflicting files)
libnautilus-extension: /usr/include/nautilus/libnautilus-extension/nautilus-column-provider.h exists in filesystem
libnautilus-extension: /usr/include/nautilus/libnautilus-extension/nautilus-column.h exists in filesystem
libnautilus-extension: /usr/include/nautilus/libnautilus-extension/nautilus-extension-types.h exists in filesystem
libnautilus-extension: /usr/include/nautilus/libnautilus-extension/nautilus-file-info.h exists in filesystem
libnautilus-extension: /usr/include/nautilus/libnautilus-extension/nautilus-info-provider.h exists in filesystem
libnautilus-extension: /usr/include/nautilus/libnautilus-extension/nautilus-location-widget-provider.h exists in filesystem
libnautilus-extension: /usr/include/nautilus/libnautilus-extension/nautilus-menu-item.h exists in filesystem
libnautilus-extension: /usr/include/nautilus/libnautilus-extension/nautilus-menu-provider.h exists in filesystem
libnautilus-extension: /usr/include/nautilus/libnautilus-extension/nautilus-menu.h exists in filesystem
libnautilus-extension: /usr/include/nautilus/libnautilus-extension/nautilus-property-page-provider.h exists in filesystem
libnautilus-extension: /usr/include/nautilus/libnautilus-extension/nautilus-property-page.h exists in filesystem
libnautilus-extension: /usr/lib/girepository-1.0/Nautilus-3.0.typelib exists in filesystem
libnautilus-extension: /usr/lib/libnautilus-extension.so exists in filesystem
libnautilus-extension: /usr/lib/libnautilus-extension.so.1 exists in filesystem
libnautilus-extension: /usr/lib/libnautilus-extension.so.1.4.0 exists in filesystem
libnautilus-extension: /usr/lib/pkgconfig/libnautilus-extension.pc exists in filesystem
libnautilus-extension: /usr/share/gir-1.0/Nautilus-3.0.gir exists in filesystem
libnautilus-extension: /usr/share/gtk-doc/html/libnautilus-extension/NautilusColumn.html exists in filesystem
libnautilus-extension: /usr/share/gtk-doc/html/libnautilus-extension/NautilusColumnProvider.html exists in filesystem
libnautilus-extension: /usr/share/gtk-doc/html/libnautilus-extension/NautilusFileInfo.html exists in filesystem
libnautilus-extension: /usr/share/gtk-doc/html/libnautilus-extension/NautilusInfoProvider.html exists in filesystem
libnautilus-extension: /usr/share/gtk-doc/html/libnautilus-extension/NautilusLocationWidgetProvider.html exists in filesystem
libnautilus-extension: /usr/share/gtk-doc/html/libnautilus-extension/NautilusMenu.html exists in filesystem
libnautilus-extension: /usr/share/gtk-doc/html/libnautilus-extension/NautilusMenuItem.html exists in filesystem
libnautilus-extension: /usr/share/gtk-doc/html/libnautilus-extension/NautilusMenuProvider.html exists in filesystem
libnautilus-extension: /usr/share/gtk-doc/html/libnautilus-extension/NautilusPropertyPage.html exists in filesystem
libnautilus-extension: /usr/share/gtk-doc/html/libnautilus-extension/NautilusPropertyPageProvider.html exists in filesystem
libnautilus-extension: /usr/share/gtk-doc/html/libnautilus-extension/ch01.html exists in filesystem
libnautilus-extension: /usr/share/gtk-doc/html/libnautilus-extension/home.png exists in filesystem
libnautilus-extension: /usr/share/gtk-doc/html/libnautilus-extension/index.html exists in filesystem
libnautilus-extension: /usr/share/gtk-doc/html/libnautilus-extension/ix01.html exists in filesystem
libnautilus-extension: /usr/share/gtk-doc/html/libnautilus-extension/left-insensitive.png exists in filesystem
libnautilus-extension: /usr/share/gtk-doc/html/libnautilus-extension/left.png exists in filesystem
libnautilus-extension: /usr/share/gtk-doc/html/libnautilus-extension/libnautilus-extension-NautilusModule.html exists in filesystem
libnautilus-extension: /usr/share/gtk-doc/html/libnautilus-extension/libnautilus-extension.devhelp2 exists in filesystem
libnautilus-extension: /usr/share/gtk-doc/html/libnautilus-extension/pt01.html exists in filesystem
libnautilus-extension: /usr/share/gtk-doc/html/libnautilus-extension/right-insensitive.png exists in filesystem
libnautilus-extension: /usr/share/gtk-doc/html/libnautilus-extension/right.png exists in filesystem
libnautilus-extension: /usr/share/gtk-doc/html/libnautilus-extension/style.css exists in filesystem
libnautilus-extension: /usr/share/gtk-doc/html/libnautilus-extension/up-insensitive.png exists in filesystem
libnautilus-extension: /usr/share/gtk-doc/html/libnautilus-extension/up.png exists in filesystem
Errors occurred, no packages were upgraded.

The output of pacman -Qkk:

error: error while reading file /var/lib/pacman/local/libisoburn-1.4.8-2/mtree: Unrecognized archive format
error: error while reading file /var/lib/pacman/local/libixion-0.13.0-1/mtree: Unrecognized archive format
error: error while reading file /var/lib/pacman/local/libmediaart-1.9.4+1+ga704d0b-1/mtree: Unrecognized archive format
error: error while reading file /var/lib/pacman/local/libnautilus-extension-3.26.2-3/mtree: Unrecognized archive format


What's weird is, that the pacman log doesn't show the 'conflicting files' error, that I got when I tried to install the package. It just logs " Running 'pacman -S libnautilus-extension'" as if it worked

cat /var/log/pacman.log

[2018-02-28 20:56] [PACMAN] Running 'pacman -S libnautilus-extension'
[2018-02-28 21:04] [PACMAN] Running 'pacman -R libnautilus-extension'
[2018-02-28 21:05] [PACMAN] Running 'pacman -R libnautilus-extension nautilus'
[2018-02-28 21:05] [PACMAN] Running 'pacman -Rc libnautilus-extension'
[2018-02-28 21:05] [ALPM] transaction started
[2018-02-28 21:05] [ALPM] removed gnome-tweak-tool (3.26.4-1)
[2018-02-28 21:05] [ALPM] removed nautilus (3.26.2-3)
[2018-02-28 21:05] [ALPM] removed libnautilus-extension (3.26.2-3)
[2018-02-28 21:05] [ALPM-SCRIPTLET] ldconfig: File /usr/lib/libnautilus-extension.so is empty, not checked.
[2018-02-28 21:05] [ALPM-SCRIPTLET] ldconfig: File /usr/lib/libisoburn.so is empty, not checked.
[2018-02-28 21:05] [ALPM-SCRIPTLET] ldconfig: File /usr/lib/libixion-0.13.so is empty, not checked.
[2018-02-28 21:05] [ALPM-SCRIPTLET] ldconfig: File /usr/lib/libmediaart-2.0.so is empty, not checked.
[2018-02-28 21:05] [ALPM-SCRIPTLET] ldconfig: File /usr/lib/libmediaart-2.0.so.0 is empty, not checked.
[2018-02-28 21:05] [ALPM-SCRIPTLET] ldconfig: File /usr/lib/libnautilus-extension.so.1 is empty, not checked.
[2018-02-28 21:05] [ALPM-SCRIPTLET] ldconfig: File /usr/lib/libisoburn.so.1.105.0 is empty, not checked.
[2018-02-28 21:05] [ALPM-SCRIPTLET] ldconfig: File /usr/lib/libnautilus-extension.so.1.4.0 is empty, not checked.
[2018-02-28 21:05] [ALPM-SCRIPTLET] ldconfig: File /usr/lib/libmediaart-2.0.so.0.904.0 is empty, not checked.
[2018-02-28 21:05] [ALPM-SCRIPTLET] ldconfig: File /usr/lib/libixion-0.13.so.0.0.0 is empty, not checked.
[2018-02-28 21:05] [ALPM-SCRIPTLET] ldconfig: File /usr/lib/libixion-0.13.so.0 is empty, not checked.
[2018-02-28 21:05] [ALPM-SCRIPTLET] ldconfig: File /usr/lib/libisoburn.so.1 is empty, not checked.
[2018-02-28 21:05] [ALPM] transaction completed
[2018-02-28 21:05] [ALPM] running 'glib-compile-schemas.hook'...
[2018-02-28 21:05] [ALPM] running 'gtk-update-icon-cache.hook'...
[2018-02-28 21:05] [ALPM] running 'systemd-update.hook'...
[2018-02-28 21:05] [ALPM] running 'update-desktop-database.hook'...
[2018-02-28 21:06] [PACMAN] Running 'pacman -S gnome-tweak-tool nautilus libnautilus-extension'

That's a lot of code... Hope it's not too much

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#7 2018-02-28 21:42:51

loqs
Member
Registered: 2014-03-06
Posts: 19,113

Re: pacman error message "ldconfig: File *** is empty, not checked"

Can you check /var/lib/pacman/local/libnautilus-extension-3.26.2-3/files does it contain the files that are listed as exists in filesystem for libnautilus-extension.
If not that would explain the issue.  If pacman's internal filetracking files have become corrupted then pacman is no longer linking a package to the files it provides.
That prevents installing the package again or removing those files from the filesystem on package removal.

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#8 2018-02-28 22:20:10

freebe
Member
From: Germany
Registered: 2015-10-29
Posts: 41

Re: pacman error message "ldconfig: File *** is empty, not checked"

Thanks for the fast reply!

There is no /var/lib/pacman/local/libnautilus-extension-[...] folder (anymore? Because pacman removed it?).

If pacman's internal filetracking files have become corrupted then pacman is no longer linking a package to the files it provides.

That should not be the case, since packman is checking for the right files, then finds them already installed, and aborts the install. See log above.

I forced the install of libnautilus-extension now, via "pacman -S --force libnautilus-extension". It looks like it worked. I will wait with forcing the other pacages, see if I get other errors or unexpected behaviours. Also I would really like to understand how this happened, so I keep them as study objects for now. wink

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#9 2018-02-28 22:33:59

loqs
Member
Registered: 2014-03-06
Posts: 19,113

Re: pacman error message "ldconfig: File *** is empty, not checked"

If you have removed libisoburn-1.4.8-2 libixion-0.13.0-1 libmediaart-1.9.4+1+ga704d0b-1 as well then there is no way to check if the files database was corrupted.
Pacman will not overwrite by default files that it is not tracking or files owned by another package.  Pacman obtains a list of files to install from the new package but
if the files database for that package does not contain entries indicating the installed version of that package provided the files but they are present on the filesystem
then pacman will treat them as untracked and not overwrite them.
edit:
grammar package not packaged

Last edited by loqs (2018-02-28 22:34:56)

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#10 2018-02-28 22:59:35

freebe
Member
From: Germany
Registered: 2015-10-29
Posts: 41

Re: pacman error message "ldconfig: File *** is empty, not checked"

If you have removed libisoburn-1.4.8-2 libixion-0.13.0-1 libmediaart-1.9.4+1+ga704d0b-1 as well then there is no way to check if the files database was corrupted.

I didn't, checking the respective folders in /var/lib/pacman/local/ shows that "files" "mtree" and "desc" are empty files. Sorry, I have the habit of leaving things out of a post, that I think might not be important or when I think I solved an issue. I need to stop that and be more consistent in my posts.

Pacman will not overwrite by default files that it is not tracking or files owned by another package.  Pacman obtains a list of files to install from the new package but
if the files database for that package does not contain entries indicating the installed version of that package provided the files but they are present on the filesystem
then pacman will treat them as untracked and not overwrite them.

Thank you for the explanation! So in that case, for these three packages, does that mean that using the "--force" option is the best solution? The packages in the arch repository still have the same versions, so that shouldn't leave any relics.

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#11 2018-02-28 23:05:10

loqs
Member
Registered: 2014-03-06
Posts: 19,113

Re: pacman error message "ldconfig: File *** is empty, not checked"

Yes use --force for those packages only or you could delete all the files pacman is not tracking first.
Would recomend you also consider checking the filesystem for corruption and check the SMART status of the device providing the filesystems.
If the device is not NVME based then you could also run a SMART selftest.

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